enzyme

[German Enzym, from Medieval Greek enzūmos, leavened : Greek en-, in; see en-² + Greek zūmē, leaven, yeast.]

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Concept

Enzymes are biological catalysts, or chemicals that speed up the rate of reaction between substances without themselves being consumed in the reaction. As such, they are vital to such bodily functions as digestion, and they make possible processes that normally could not occur except at temperatures so high they would threaten the well-being of the body. A type of protein, enzymes sometimes work in tandem with non-proteins called coenzymes. Among the processes in which enzymes play a vital role is fermentation, which takes place in the production of alcohol or the baking of bread and also plays a part in numerous other natural phenomena, such as the purification of wastewater.

How It Works

Amino Acids, Proteins, and Biochemistry

Amino acids are organic compounds made of carbon, hydrogen, oxygen, nitrogen, and (in some cases) sulfur bonded in characteristic formations. Strings of 50 or more amino acids are known as proteins, large molecules that serve the functions of promoting normal growth, repairing damaged tissue, contributing to the body's immune system, and making enzymes. The latter are a type of protein that functions as a catalyst, a substance that speeds up a chemical reaction without participating in it. Catalysts, of which enzymes in the bodies of plants and animals are a good example, thus are not consumed in the reaction.

Catalysts

In a chemical reaction, substances known as reactants interact with one another to create new substances, called products. Energy is an important component in the chemical reaction, because a certain threshold, termed the activation energy, must be crossed before a reaction can occur. To increase the rate at which a reaction takes place and to hasten the crossing of the activation energy threshold, it is necessary to do one of three things.

The first two options are to increase either the concentration of reactants or the temperature at which the reaction takes place. It is not always feasible or desirable, however, to do either of these things. Many of the processes that take place in the human body, for instance, normally would require high temperatures—temperatures, in fact, that are too high to sustain human life. Imagine what would happen if the only way we had of digesting starch was to heat it to the boiling point inside our stomachs! Fortunately, there is a third option: the introduction of a catalyst, a substance that speeds up a reaction without participating in it either as a reactant or as a product. Catalysts thus are not consumed in the reaction. Enzymes, which facilitate the necessary reactions in our bodies without raising temperatures or increasing the concentrations of substances, are a prime example of a chemical catalyst.

The Discovery of Catalysis

Long before chemists recognized the existence of catalysts, ordinary people had been using the chemical process known as catalysis for numerous purposes: making soap, fermenting wine to create vinegar, or leavening bread, for instance. Early in the nineteenth century, chemists began to take note of this phenomenon. In 1812 the Russian chemist Gottlieb Kirchhoff (1764-1833) was studying the conversion of starches to sugar in the presence of strong acids when he noticed something interesting.

When a suspension of starch (that is, particles of starch suspended in water) was boiled, Kirchhoff observed, no change occurred in the starch. When he added a few drops of concentrated acid before boiling the suspension, however, he obtained a very different result. This time, the starch broke down to form glucose, a simple sugar (see Carbohydrates), whereas the acid—which clearly had facilitated the reaction—underwent no change. In 1835 the Swedish chemist Jöns Berzelius (1779-1848) provided a name to the process Kirchhoff had observed: catalysis, derived from the Greek words kata ("down") and lyein ("loosen"). Just two years earlier, in 1833, the French physiologist Anselme Payen (1795-1871) had isolated a material from malt that accelerated the conversion of starch to sugar, for instance, in the brewing of beer.

The renowned French chemist Louis Pasteur (1822-1895), who was right about so many things, called these catalysts ferments and pronounced them separate organisms. In 1897, however, the German biochemist Eduard Buchner (1860-1917) isolated the catalysts that bring about the fermentation of alcohol and determined that they were chemical substances, not organisms. By that time, the German physiologist Willy Kahne had suggested the name enzyme for these catalysts in living systems.

Substrates and Active Sites

Each type of enzyme is geared to interact chemically with only one particular substance or type of substance, termed a substrate. The two parts fit together, according to a widely accepted theory introduced in the 1890s by the German chemist Emil Fischer (1852-1919), as a key fits into a lock. Each type of enzyme has a specific three-dimensional shape that enables it to fit with the substrate, which has a complementary shape.

The link between enzymes and substrates is so strong that enzymes often are named after the substrate involved, simply by adding ase to the name of the substrate. For example, lactase is the enzyme that catalyzes the digestion of lactose, or milk sugar, and urease catalyzes the chemical breakdown of urea, a substance in urine. Enzymes bind their reactants or substrates at special folds and clefts, named active sites, in the structure of the substrate. Because numerous interactions are required in their work of catalysis, enzymes must have many active sites, and therefore they are very large, having atomic mass figures as high as one million amu. (An atomic mass unit, or amu, is approximately equal to the mass of a proton, a positively charged particle in the nucleus of an atom.)

Suppose a substrate molecule, such as a starch, needs to be broken apart for the purposes of digestion in a living body. The energy needed to break apart the substrate is quite large, larger than is available in the body. An enzyme with the correct molecular shape arrives on the scene and attaches itself to the substrate molecule, forming a chemical bond within it. The formation of these bonds causes the breaking apart of other bonds within the substrate molecule, after which the enzyme, its work finished, moves on to another uncatalyzed substrate molecule.

Coenzymes

All enzymes belong to the protein family, but many of them are unable to participate in a catalytic reaction until they link with a non protein component called a coenzyme. This can be a medium-size molecule called a prosthetic group, or it can be a metal ion (an atom with a net electric charge), in which case it is known as a cofactor. Quite often, though, coenzymes are composed wholly or partly of vitamins. Although some enzymes are attached very tightly to their coenzymes, others can be parted easily; in either case, the parting almost always deactivates both partners.

The first coenzyme was discovered by the English biochemist Sir Arthur Harden (1865-1940) around the turn of the nineteenth century. Inspired by Buchner, who in 1897 had detected an active enzyme in yeast juice that he had named zymase, Harden used an extract of yeast in most of his studies. He soon discovered that even after boiling, which presumably destroyed the enzymes in yeast, such deactivated yeast could be reactivated. This finding led Harden to the realization that a yeast enzyme apparently consists of two parts: a large, molecular portion that could not survive boiling and was almost certainly a protein and a smaller portion that had survived and was probably not a protein. Harden, who later shared the 1929 Nobel Prize in chemistry for this research, termed the non protein a coferment, but others began calling it a coenzyme.

Real-Life Applications

The Body, Food, and Digestion

Enzymes enable the many chemical reactions that are taking place at any second inside the body of a plant or animal. One example of an enzyme is cytochrome, which aids the respiratory system by catalyzing the combination of oxygen with hydrogen within the cells. Other enzymes facilitate the conversion of food to energy and make possible a variety of other necessary biological functions. Enzymes in the human body fulfill one of three basic functions. The largest of all enzyme types, sometimes called metabolic enzymes, assist in a wide range of basic bodily processes, from breathing to thinking. Some such enzymes are devoted to maintaining the immune system, which protects us against disease, and others are involved in controlling the effects of toxins, such as tobacco smoke, converting them to forms that the body can expel more easily.

A second category of enzyme is in the diet and consists of enzymes in raw foods that aid in the process of digesting those foods. They include proteases, which implement the digestion of protein; lipases, which help in digesting lipids or fats; and amylases, which make it possible to digest carbohydrates. Such enzymes set in motion the digestive process even when food is still in the mouth. As these enzymes move with the food into the upper portion of the stomach, they continue to assist with digestion.

The third group of enzymes also is involved in digestion, but these enzymes are already in the body. The digestive glands secrete juices containing enzymes that break down nutrients chemically into smaller molecules that are more easily absorbed by the body. Amylase in the saliva begins the process of breaking down complex carbohydrates into simple sugars. While food is still in the mouth, the stomach begins producing pepsin, which, like protease, helps digest protein.

Later, when food enters the small intestine, the pancreas secretes pancreatic juice—which contains three enzymes that break down carbohydrates, fats, and proteins—into the duodenum, which is part of the small intestine. Enzymes from food wind up among the nutrients circulated to the body through plasma, a watery liquid in which red blood cells are suspended. These enzymes in the blood assist the body in everything from growth to protection against infection.

One digestive enzyme that should be in the body, but is not always present, is lactase. As we noted earlier, lactase works on lactose, the principal carbohydrate in milk, to implement its digestion. If a person lacks this enzyme, consuming dairy products may cause diarrhea, bloating, and cramping. Such a person is said to be "lactose intolerant," and if he or she is to consume dairy products at all, they must be in forms that contain lactase. For this reason, Lactaid milk is sold in the specialty dairy section of major supermarkets, while many health-food stores sell lactaid tablets.

Fermentation

Fermentation, in its broadest sense, is a process involving enzymes in which a compound rich in energy is broken down into simpler substances. It also is sometimes identified as a process in which large organic molecules (those containing hydrogen and carbon) are broken down into simpler molecules as the result of the action of microorganisms working anaerobically, or in the absence of oxygen. The most familiar type of fermentation is the conversion of sugars and starches to alcohol by enzymes in yeast. To distinguish this reaction from other kinds of fermentation, the process is sometimes termed alcoholic or ethanolic fermentation.

At some point in human prehistory, humans discovered that foods spoil, or go bad. Yet at the dawn of history—that is, in ancient Sumer and Egypt—people found that sometimes the "spoilage" (that is, fermentation) of products could have beneficial results. Hence the fermentation of fruit juices, for example, resulted in the formation of primitive forms of wine. Over the centuries that followed, people learned how to make both alcoholic beverages and bread through the controlled use of fermentation.

Alcoholic Beverages

In fermentation, starch is converted to simple sugars, such as sucrose and glucose, and through a complex sequence of some 12 reactions, these sugars then are converted to ethyl alcohol (the kind of alcohol that can be consumed, as opposed to methyl alcohol and other toxic forms) and carbon dioxide. Numerous enzymes are needed to carry out this sequence of reactions, the most important being zymase, which is found in yeast cells. These enzymes are sensitive to environmental conditions, such that when the concentration of alcohol reaches about 14%, they are deactivated. For this reason, no fermentation product (such as wine) can have an alcoholic concentration of more than about 14%. Stronger alcoholic beverages, such as whisky, are the result of another process, distillation.

The alcoholic beverages that can be produced by fermentation vary widely, depending primarily on two factors: the plant that is fermented and the enzymes used for fermentation. Depending on the materials available to them, various peoples have used grapes, berries, corn, rice, wheat, honey, potatoes, barley, hops, cactus juice, cassava roots, and other plant materials for fermentation to produce wines, beers, and other fermented drinks. The natural product used in making the beverage usually determines the name of the synthetic product. Thus, for instance, wine made with rice—a time-honored tradition in Japan—is known as sake, while a fermented beverage made from barley, hops, or malt sugar has a name very familiar to Americans: beer. Grapes make wine, but "wine" made from honey is known as mead.

Other Foods

Of course, ethyl alcohol is not the only useful product of fermentation or even of fermentation using yeast; so, too, are baked goods, such as bread. The carbon dioxide generated during fermentation is an important component of such items. When the batter for bread is mixed, a small amount of sugar and yeast is added. The bread then rises, which is more than just a figure of speech: it actually puffs up as a result of the fermentation of the sugar by enzymes in the yeast, which brings about the formation of carbon dioxide gas. The carbon dioxide gives the batter bulkiness and texture that would be lacking without the fermentation process. Another food-related application of fermentation is the production of one processed type of food from a raw, natural variety. The conversion of raw olives to the olives sold in stores, of cucumbers to pickles, and of cabbage to sauerkraut utilizes a particular bacterium that assists in a type of fermentation.

Industrial Applications

There is even ongoing research into the creation of edible products from the fermentation of petroleum. While this may seem a bit far-fetched, it is less difficult to comprehend powering cars with an environmentally friendly product of fermentation known as gasohol. Gasohol first started to make headlines in the 1970s, when an oil embargo and resulting increases in gas prices, combined with growing environmental concerns, raised the need for a type of fuel that would use less petroleum. A mixture of about 90% gasoline and 10% alcohol, gasohol burns more cleanly that gasoline alone and provides a promising method for using renewable resources (plant material) to extend the availability of a nonrenewable resource (petroleum). Furthermore, the alcohol needed for this product can be obtained from the fermentation of agricultural and municipal wastes.

The applications of fermentation span a wide spectrum, from medicines that go into people's bodies to the cleaning of waters containing human waste. Some antibiotics and other drugs are prepared by fermentation: for example, cortisone, used in treating arthritis, can be made by fermenting a plant steroid known as diosgenin. In the treatment of wastewater, anaerobic, or non-oxygen-dependent, bacteria are used to ferment organic material. Thus, solid wastes are converted to carbon dioxide, water, and mineral salts.

Where to Learn More

Asimov, Isaac. The Chemicals of Life: Enzymes, Vitamins, Hormones. New York: Abelard-Schulman, 1954.

"Enzymes: Classification, Structure, Mechanism." Washington State University Department of Chemistry (Web site). <http://www.chem.wsu.edu/Chem102/102-EnzStrClassMech.html>.

"Enzymes." HordeNet: Hardy Research Group, Department of Chemistry, The University of Akron (Web site). <http://ull.chemistry.uakron.edu/genobc/Chapter_20/>.

Fruton, Joseph S. A Skeptical Biochemist. Cambridge, MA: Harvard University Press, 1992.

"Introduction to Enzymes." Worthington Biochemical Corporation (Web site). <http://www.worthingtonbiochem.com/introBiochem/introEnzymes.html>.

Kornberg, Arthur. For the Love of Enzymes: The Odyssey of a Biochemist. Cambridge, MA: Harvard University Press, 1989.

"Milk Makes Me Sick: Exploration of the Basis of Lactose Intolerance." Exploratorium: The Museum of Science, Art, and Human Perception (Web site). <http://www.exploratorium.edu/snacks/milk_makes-me_sick/>.

A catalytic protein produced by living cells. The chemical reactions involved in the digestion of foods, the biosynthesis of macromolecules, the controlled release and utilization of chemical energy, and other processes characteristic of life are all catalyzed by enzymes. In the absence of enzymes, these reactions would not take place at a significant rate. Several hundred different reactions can proceed simultaneously within a living cell, and the cell contains a comparable number of individual enzymes, each of which controls the rate of one or more of these reactions. The potentiality of a cell for growing, dividing, and performing specialized functions, such as contraction or transmission of nerve impulses, is determined by the complement of enzymes it possesses. Some representative enzymes, their sources, and reaction specificities are shown in the table.

Characteristics

Enzymes can be isolated and are active outside the living cell. They are such efficient catalysts that they accelerate chemical reactions measurably, even at concentrations so low that they cannot be detected by most chemical tests for protein. Like other chemical reactions, enzyme-catalyzed reactions proceed only when accompanied by a decrease in free energy; at equilibrium the concentrations of reactants and products are the same in the presence of an enzyme as in its absence. An enzyme can catalyze an indefinite amount of chemical change without itself being diminished or altered by the reaction. However, because most isolated enzymes are relatively unstable, they often gradually lose activity under the conditions employed for their study.

Chemical nature

All enzymes are proteins. Their molecular weights range from about 10,000 to more than 1,000,000. Like other proteins, enzymes consist of chains of amino acids linked together by peptide bonds. An enzyme molecule may contain one or more of these polypeptide chains. The sequence of amino acids within the polypeptide chains is characteristic for each enzyme and is believed to determine the unique three-dimensional conformation in which the chains are folded. This conformation, which is necessary for the activity of the enzyme, is stabilized by interactions of amino acids in different parts of the peptide chains with each other and with the surrounding medium. These interactions are relatively weak and may be disrupted readily by high temperatures, acid or alkaline conditions, or changes in the polarity of the medium. Such changes lead to an unfolding of the peptide chains (denaturation) and a concomitant loss of enzymatic activity, solubility, and other properties characteristic of the native enzyme. Enzyme denaturation is sometimes reversible. See also Amino acids; Protein.

Many enzymes contain an additional, nonprotein component, termed a coenzyme or prosthetic group. This may be an organic molecule, often a vitamin derivative, or a metal ion. The coenzyme, in most instances, participates directly in the catalytic reaction. For example, it may serve as an intermediate carrier of a group being transferred from one substrate to another. Some enzymes have coenzymes that are tightly bound to the protein and difficult to remove, while others have coenzymes that dissociate readily. When the protein moiety (the apoenzyme) and the coenzyme are separated from each other, neither possesses the catalytic properties of the original conjugated protein (the holoenzyme). By simply mixing the apoenzyme and the coenzyme together, the fully active holoenzyme can often be reconstituted. The same coenzyme may be associated with many enzymes which catalyze different reactions. It is thus primarily the nature of the apoenzyme rather than that of the coenzyme which determines the specificity of the reaction. See also Coenzyme.

The complete amino acid sequence of several enzymes has been determined by chemical methods. By x-ray crystallographic methods even the exact three-dimensional molecular structure of a few enzymes has been deduced. See also X-ray crystallography.

Classification and nomenclature

Enzymes are usually classified and named according to the reaction they catalyze. The principal classes are as follows.

Oxidoreductases catalyze reactions involving electron transfer, and play an important role in cellular respiration and energy production. Some of them participate in the process of oxidative phosphorylation, whereby the energy released by the oxidation of carbohydrates and fats is utilized for the synthesis of adenosine triphosphate (ATP) and thus made directly available for energy-requiring reactions.

Transferases catalyze the transfer of a particular chemical group from one substance to another. Thus, transaminases transfer amino groups, transmethylases transfer methyl groups, and so on. An important subclass of this group are the kinases, which catalyze the phosphorylation of their substrates by transferring a phosphate group, usually from ATP, thereby activating an otherwise metabolically inert compound for further transformations.

Hydrolases catalyze the hydrolysis of proteins (proteinases and peptidases), nucleic acids (nucleases), starch (amylases), fats (lipases), phosphate esters (phosphatases), and other substances. Many hydrolases are secreted by the stomach, pancreas, and intestine and are responsible for the digestion of foods. Others participate in more specialized cellular functions. For example, cholinesterase, which catalyzes the hydrolysis of acetylcholine, plays an important role in the transmission of nervous impulses. See also Acetylcholine.

Lyases catalyze the nonhydrolytic cleavage of their substrate with the formation of a double bond. Examples are decarboxylases, which remove carboxyl groups as carbon dioxide, and dehydrases, which remove a molecule of water. The reverse reactions are catalyzed by the same enzymes.

Isomerases catalyze the interconversion of isomeric compounds.

Ligases, or synthetases, catalyze endergonic syntheses coupled with the exergonic hydrolysis of ATP. They allow the chemical energy stored in ATP to be utilized for driving reactions uphill.

Specificity

The majority of enzymes catalyze only one type of reaction and act on only one compound or on a group of closely related compounds. There must exist between an enzyme and its substrate a close fit, or complementarity. In many cases, a small structural change, even in a part of the molecule remote from that altered by the enzymatic reaction, abolishes the ability of a compound to serve as a substrate. An example of an enzyme highly specific for a single substrate is urease, which catalyzes the hydrolysis of urea to carbon dioxide and ammonia. On the other hand, some enzymes exhibit a less restricted specificity and act on a number of different compounds that possess a particular chemical group. This is termed group specificity.

A remarkable property of many enzymes is their high degree of stereospecificity, that is, their ability to discriminate between asymmetric molecules of the right-handed and left-handed configurations. An example of a stereospecific enzyme is L-amino acid oxidase. This enzyme catalyzes the oxidation of a variety of amino acids of the type R—CH(NH₂)COOH. The rate of oxidation varies greatly, depending on the nature of the R group, but only amino acids of the L configuration react. See also Stereochemistry.

Enzymes are most familiarly associated with digestion, as substances in the alimentary tract that are necessary for the breakdown of food into simpler stuffs that can be absorbed into the body proper. These are indeed important, but they are in a small minority among the vast population of the body's enzymes. They also differ from the majority in acting outside rather than inside the cells that make them.

All living cells are teeming with enzymes. The name comes from the Greek meaning ‘in leaven’ or yeast. They are proteins, synthesized in cells, which act as catalysts, causing all the body's chemical processes to advance with the necessary rapidity and completeness. Enzymes are ubiquitous in body cells and fluids, and they are specific — each enzyme is responsible for catalyzing one particular chemical process. Their existence and their function came to be recognized during the nineteenth century; understanding advanced with burgeoning twentieth-century biochemistry; and molecular biologists continue to elucidate their ultimate structure and mode of action, and the genes that make them.

The names and nature of enzymes

The naming of enzymes in most cases reveals their function; ‘-ase’ is added to the name either of the substance (the substrate) on which they act (like peptidase for those acting on peptides), or of the type of reaction induced (such as hydrolase, for those causing hydrolysis, the splitting of a substance with addition of water, or transferase, for those moving some chemical group from one molecule to another). Some of the first enzymes to be discovered have unique names, such as pepsin in the stomach, and trypsin from the pancreas, which are both proteinases.

So what sort of proteins are they, and how do they function? With molecular masses of 10 000 to 1 000 000, enzymes are themselves large molecules, but some also exist in larger complexes that facilitate a sequence of changes. An enzyme molecule is a ‘globular’ protein that has an area on its surface to which can be bound only the specific substrate that the enzyme is designed to accept. This binding leads to changes in both molecules that result in the formation of the required product, and restoration of the enzyme molecule to its original state, ready to take on another substrate molecule. With progressively higher concentrations of substrate the rate of product yield increases, but the increment in rate diminishes as it approaches a maximum at a certain substrate concentration; beyond this point only an increase in the concentration of the enzyme itself can accelerate the process. This behaviour is consistent with progressive occupation of binding sites on all available enzymes, until they are all functioning at a maximal turnover rate.

Range and sites of enzyme function

Enzymes operate at every stage of life. Even the head of the sperm releases an enzyme that dissolves its path through the outer covering of the ovum to reach and penetrate it. Cell division in the embryo and throughout life involves replication of the DNA that carries the genetic information. A series of specific enzymes is needed for this, to unwind the double helix, to replicate it by the synthesis of new strands, and to put it and the new pairs back together again — whilst other enzymes meanwhile supply energy by the breakdown of adenosine triphosphate (ATP). Yet others are involved in the formation of messenger RNA and in all subsequent synthesis of proteins in a cell that results from the genetic coding.

Enzymes implement every event in the internal life of every cell in the body, and in its interaction with its environment. Each enzyme, or chain of enzymes acting in rapid sequence, has a specific function. There are those that are necessary for respiration and energy production; for transport mechanisms across the cell membrane and between internal components; for modifications of cellular metabolism in response to hormones; and for any specialized activity, including secretion by glandular cells, contraction by muscle cells, synthesis, release, and reuptake of neurotransmitters by nerve cells. The continual potential damage to tissues by the generation of free radicals is crucially limited by the body's antioxidant enzymes.

All cells have enzymes in their membrane, in the cytoplasm, and in the organelles within them. Those at the heart of cellular metabolism are the complex sequence of respiratory enzymes in the mitochondria that make possible the utilization of oxygen for the conversion of nutrient substrates to carbon dioxide and water, synthesis of ATP, and its breakdown for release of energy.

Cell membranes are furnished with ‘sodium pumps’ — protein molecules spanning the cell membrane that pump sodium ions out and potassium ions in. Facing inwards is an enzyme site that binds and breaks down ATP to supply the energy for pumping. Other enzyme molecules in the cell membrane may have, in addition to a site for substrate-binding, another that acts as receptor for a ‘messenger’ that activates the catalytic process: for example, the insulin receptor spans the cell membrane of muscle or fat cells; its outer site binds insulin, and its inner site handles the first of a series of enzyme-catalyzed reactions inside the cell that result in the several effects of insulin.

At synapses between nerves, and at neuromuscular junctions, enzymes are present that break down redundant neurotransmitters, preventing persistence of their effects. An example is acetylcholinesterase, found in the synaptic clefts on motor end plates in skeletal muscle, which hydrolyses excess acetylcholine, the neurotransmitter released by the motor nerve terminals.

Within skeletal muscle fibres, the enzymes vary according to their type of metabolism: whether it is predominantly aerobic (utilizing oxygen: ‘slow’ or ‘red’ muscle) or anaerobic (‘fast’ or ‘pale’ muscle). The sequence of events leading from activation of a muscle fibre by neurotransmitter, to contraction by means of interaction between myosin and actin filaments, depends on enzymes at every stage.

Enzymes in the blood

In the circulating blood there are enzymes both inside the blood cells, and outside in the plasma. Blood cells, in common with all cells, have the necessary enzymes for membrane transport and energy production. White blood cells have respiratory enzymes for aerobic metabolism, and others suited to their particular functions. Red blood cells are without mitochondria and respire anaerobically, so have enzymes appropriate to anaerobic glycolysis. Important for their function in whole-body respiratory gas exchange, they contain carbonic anhydrase, which promotes the uptake from the tissues of carbon dioxide and its carriage in the blood as bicarbonate, by catalyzing its combination with water to form carbonic acid, and its release in the lungs by this reaction in reverse.

Some enzymes exist as pro-enzymes or zymogens; they require some molecular change to be triggered into their active forms. These include proteins in the plasma that are involved in blood clotting: prothrombin is synthesized in the liver, and becomes thrombin when clotting is activated, and plasminogen can come into action as plasmin, a clot-dissolving enzyme. In the stomach, pepsinogen is secreted, and activated into pepsin by the acid that is secreted at the same site.

Enzymes that are normally secreted only into the gut or inside cells may, in pathological conditions, appear in significant quantities in the plasma, so that their measurement may be clinically useful. Examples are digestive enzymes that leak into the blood in acute pancreatitis, and creatine kinase, an enzyme from muscle tissue, that can appear in skeletal muscle disorders or, along with other intracellular enzymes, after a coronary thrombosis resulting in breakdown of some of the cardiac muscle.

Conditions for enzyme activity

All enzymes need the right environment for effective function, notably an optimal acidity, which differs in accordance with the site at which a particular enzyme acts (for example, more acidic inside cells than outside, and, for digestive enzymes, acidic in the stomach and alkaline in the duodenum). Like any chemical reactions, the rate of those that are catalyzed by enzymes varies with temperature. Local heat generation, for example in exercising muscle, enhances all such reactions within it. Likewise, whole-body metabolic rate increases in fever and decreases in hypothermia, because of the effect on all enzyme-catalyzed reactions. Extremes of pH or temperature irreversibly abolish enzyme activity, and so also do some substances that bind to the active sites of particular enzymes. These include an organophosphate ‘nerve gas’ that blocks acetylcholinesterase (causing persistent accumulation of acetylcholine at neuromuscular junctions, and thus uncontrollable muscle contraction). Poisoning by cyanide is due to blocking an essential enzyme in mitochondria and so fatally preventing all tissue respiration.

Medical applications

It is possible to inhibit the action of an enzyme without destroying it, and this has important therapeutic implications. There are substances that compete with the natural substrate for binding to an enzyme by having a similar structure, and others that act on other components of the enzyme molecule, preventing its ability to catalyze. Acetylcholinesterase inhibition is again an example — though in this context useful and reversible — in the treatment of the condition of myasthenia gravis, when the receptors on muscles cells for acetylcholine are deficient; the similar molecular structure of neostigmine allows it to bind to the enzyme, preventing binding and breakdown of acetylcholine; this can then accumulate sufficiently to enhance neuromuscular transmission. Drugs are used similarly to reverse the neuromuscular blockade deliberately induced during general anaesthesia. A different and important medical application of enzyme inhibition is in the use of antibiotics that block enzymes in microorganisms that are essential for their life or growth.

There are also many necessary co-enzymes, or co-factors for enzymes — organic non-protein molecules, smaller than the enzymes themselves, which either enhance or are necessary for the enzyme's activity. These again are widespread throughout the body, and are of many different molecular structures. Some require for their synthesis small amounts of essential substances from the diet. This is the basis of the need for the vitamins of the B group — they provide components for co-enzymes which could not otherwise be made in the body. Ions of several metals are also essential as co-factors, as well as for incorporation in some enzyme molecules themselves.

— Sheila Jennett

See also alimentary system; cell; cell membrane; metabolism; respiration; transport.

A protein that catalyses a metabolic reaction, so increasing its rate. Enzymes are specific for both the compounds acted on (the substrates) and the reactions carried out. Because of this, enzymes extracted from plants, animals, or micro-organisms, or those produced by genetic manipulation are widely used in the chemical, pharmaceutical, and food industries (e.g. chymosin in cheese making, maltase in beer production, for synthesis of vitamin C and citric acid).

Because they are proteins, enzymes are permanently inactivated by heat, strong acid or alkali, and other conditions which cause denaturation of proteins.

Many enzymes contain non-protein components which are essential for their function. These are known as prosthetic groups, coenzymes, or cofactors, and may be metal ions, metal ions in organic combination (e.g. haem in haemoglobin and cytochromes) or a variety of organic compounds, many of which are derived from vitamins. The (inactive) protein without its prosthetic group is known as the apo-enzyme, and the active assembly of protein plus prosthetic group is the holo-enzyme. See also enzyme activation assays.

Enzymes are proteins which act as biological catalysts accelerating specific chemical reactions, such as the digestion of food. Without enzymes, these reactions often require very high temperatures and pressures. Although enzymes take part in the reactions, they are not chemically altered by them. Consequently they are not used up and are required in relatively small concentrations. The body varies the concentration of a particular enzyme to regulate a specific activity; generally, the higher the enzyme concentration, the greater the rate of reaction.

Enzymes sometimes require additional, non-protein components to function properly; these are called cofactors. Many minerals and vitamins function as cofactors or coenzymes; deficiencies result in inefficient enzyme activity and ill health.

Enzymes work most effectively within narrow ranges of temperature and pH. Deviations cause the enzyme to change shape (denaturation) and to become less effective; this happens if the body overheats as a result of physical exertion or when lactic acid produced by anaerobic respiration lowers the pH of body fluids.

A protein substance that acts as a catalyst to speed up metabolic and other processes involving organic materials. Some enzymes function within cells; others function in the extracellular fluids and tissue spaces and organs. They are active in all major tissue functions, such as cellular respiration, muscle contraction, digestive processes, and energy consumption, and are produced intracellularly.

A protein that acts as a biological catalyst, accelerating the rate of specific biochemical reactions. An enzyme is not used up or changed in the reaction, and the enzyme cannot force a reaction to occur between molecules that would not otherwise react. Enzymes are denatured with time, and by changes in pH and temperature. The concentration of specific enzymes involved in energy systems, is an important determinant of athletic ability.

Enzymes are proteins that act as biological catalysts. They decrease the amount of energy needed (activation energy) to start a metabolic reaction. Without enzymes, you would not be able to harvest energy and nutrients from your food. As an example, lactose intolerance is an inability to produce lactase, the enzyme that breaks down milk sugar (lactose). While this condition is not life-threatening for adults, it can have severe consequences for infants and children.

A protein molecule that helps other organic molecules enter into chemical reactions with one another but is itself unaffected by these reactions. In other words, enzymes act as catalysts for organic biochemical reactions.

"Biocatalyst" redirects here. For the use of natural catalysts to perform chemical transformations on organic compounds, see Biocatalysis.

Human glyoxalase I. Two zinc ions that are needed for the enzyme to catalyze its reaction are shown as purple spheres, and an enzyme inhibitor called S-hexylglutathione is shown as a space-filling model, filling the two active sites.

Enzymes are proteins that catalyze (i.e., increase the rates of) chemical reactions.^[1][2] In enzymatic reactions, the molecules at the beginning of the process are called substrates, and the enzyme converts them into different molecules, called the products. Almost all processes in a biological cell need enzymes to occur at significant rates. Since enzymes are selective for their substrates and speed up only a few reactions from among many possibilities, the set of enzymes made in a cell determines which metabolic pathways occur in that cell.

Like all catalysts, enzymes work by lowering the activation energy (E_a^‡) for a reaction, thus dramatically increasing the rate of the reaction. Most enzyme reaction rates are millions of times faster than those of comparable un-catalyzed reactions. As with all catalysts, enzymes are not consumed by the reactions they catalyze, nor do they alter the equilibrium of these reactions. However, enzymes do differ from most other catalysts by being much more specific. Enzymes are known to catalyze about 4,000 biochemical reactions.^[3] A few RNA molecules called ribozymes also catalyze reactions, with an important example being some parts of the ribosome.^[4][5] Synthetic molecules called artificial enzymes also display enzyme-like catalysis.^[6]

Enzyme activity can be affected by other molecules. Inhibitors are molecules that decrease enzyme activity; activators are molecules that increase activity. Many drugs and poisons are enzyme inhibitors. Activity is also affected by temperature, chemical environment (e.g., pH), and the concentration of substrate. Some enzymes are used commercially, for example, in the synthesis of antibiotics. In addition, some household products use enzymes to speed up biochemical reactions (e.g., enzymes in biological washing powders break down protein or fat stains on clothes; enzymes in meat tenderizers break down proteins, making the meat easier to chew).

Contents 1 Etymology and history 2 Structures and mechanisms 2.1 Specificity 2.1.1 "Lock and key" model 2.1.2 Induced fit model 2.2 Mechanisms 2.2.1 Transition State Stabilization 2.2.2 Dynamics and function 2.3 Allosteric modulation 3 Cofactors and coenzymes 3.1 Cofactors 3.2 Coenzymes 4 Thermodynamics 5 Kinetics 6 Inhibition 7 Biological function 8 Control of activity 9 Involvement in disease 10 Naming conventions 11 Industrial applications 12 See also 13 References 14 Further reading 15 External links

Etymology and history

Eduard Buchner

As early as the late 1700s and early 1800s, the digestion of meat by stomach secretions^[7] and the conversion of starch to sugars by plant extracts and saliva were known. However, the mechanism by which this occurred had not been identified.^[8]

In the 19th century, when studying the fermentation of sugar to alcohol by yeast, Louis Pasteur came to the conclusion that this fermentation was catalyzed by a vital force contained within the yeast cells called "ferments", which were thought to function only within living organisms. He wrote that "alcoholic fermentation is an act correlated with the life and organization of the yeast cells, not with the death or putrefaction of the cells."^[9]

In 1878, German physiologist Wilhelm Kühne (1837–1900) first used the term enzyme, which comes from Greek ενζυμον, "in leaven", to describe this process. The word enzyme was used later to refer to nonliving substances such as pepsin, and the word ferment was used to refer to chemical activity produced by living organisms.

In 1897, Eduard Buchner began to study the ability of yeast extracts that lacked any living yeast cells to ferment sugar. In a series of experiments at the University of Berlin, he found that the sugar was fermented even when there were no living yeast cells in the mixture.^[10] He named the enzyme that brought about the fermentation of sucrose "zymase".^[11] In 1907, he received the Nobel Prize in Chemistry "for his biochemical research and his discovery of cell-free fermentation". Following Buchner's example, enzymes are usually named according to the reaction they carry out. Typically, to generate the name of an enzyme, the suffix -ase is added to the name of its substrate (e.g., lactase is the enzyme that cleaves lactose) or the type of reaction (e.g., DNA polymerase forms DNA polymers).

Having shown that enzymes could function outside a living cell, the next step was to determine their biochemical nature. Many early workers noted that enzymatic activity was associated with proteins, but several scientists (such as Nobel laureate Richard Willstätter) argued that proteins were merely carriers for the true enzymes and that proteins per se were incapable of catalysis. However, in 1926, James B. Sumner showed that the enzyme urease was a pure protein and crystallized it; Sumner did likewise for the enzyme catalase in 1937. The conclusion that pure proteins can be enzymes was definitively proved by Northrop and Stanley, who worked on the digestive enzymes pepsin (1930), trypsin and chymotrypsin. These three scientists were awarded the 1946 Nobel Prize in Chemistry.^[12]

This discovery that enzymes could be crystallized eventually allowed their structures to be solved by x-ray crystallography. This was first done for lysozyme, an enzyme found in tears, saliva and egg whites that digests the coating of some bacteria; the structure was solved by a group led by David Chilton Phillips and published in 1965.^[13] This high-resolution structure of lysozyme marked the beginning of the field of structural biology and the effort to understand how enzymes work at an atomic level of detail.

Structures and mechanisms

See also: Enzyme catalysis

Ribbon diagram showing carbonic anhydrase II. The grey sphere is the zinc cofactor in the active site. Diagram drawn from PDB 1MOO.

Enzymes are generally globular proteins and range from just 62 amino acid residues in size, for the monomer of 4-oxalocrotonate tautomerase,^[14] to over 2,500 residues in the animal fatty acid synthase.^[15] A small number of RNA-based biological catalysts exist, with the most common being the ribosome; these are referred to as either RNA-enzymes or ribozymes. The activities of enzymes are determined by their three-dimensional structure.^[16] However, although structure does determine function, predicting a novel enzyme's activity just from its structure is a very difficult problem that has not yet been solved.^[17]

Most enzymes are much larger than the substrates they act on, and only a small portion of the enzyme (around 3–4 amino acids) is directly involved in catalysis.^[18] The region that contains these catalytic residues, binds the substrate, and then carries out the reaction is known as the active site. Enzymes can also contain sites that bind cofactors, which are needed for catalysis. Some enzymes also have binding sites for small molecules, which are often direct or indirect products or substrates of the reaction catalyzed. This binding can serve to increase or decrease the enzyme's activity, providing a means for feedback regulation.

Like all proteins, enzymes are made as long, linear chains of amino acids that fold to produce a three-dimensional product. Each unique amino acid sequence produces a specific structure, which has unique properties. Individual protein chains may sometimes group together to form a protein complex. Most enzymes can be denatured—that is, unfolded and inactivated—by heating or chemical denaturants, which disrupt the three-dimensional structure of the protein. Depending on the enzyme, denaturation may be reversible or irreversible.

Specificity

Enzymes are usually very specific as to which reactions they catalyze and the substrates that are involved in these reactions. Complementary shape, charge and hydrophilic/hydrophobic characteristics of enzymes and substrates are responsible for this specificity. Enzymes can also show impressive levels of stereospecificity, regioselectivity and chemoselectivity.^[19]

Some of the enzymes showing the highest specificity and accuracy are involved in the copying and expression of the genome. These enzymes have "proof-reading" mechanisms. Here, an enzyme such as DNA polymerase catalyzes a reaction in a first step and then checks that the product is correct in a second step.^[20] This two-step process results in average error rates of less than 1 error in 100 million reactions in high-fidelity mammalian polymerases.^[21] Similar proofreading mechanisms are also found in RNA polymerase,^[22] aminoacyl tRNA synthetases^[23] and ribosomes.^[24]

Some enzymes that produce secondary metabolites are described as promiscuous, as they can act on a relatively broad range of different substrates. It has been suggested that this broad substrate specificity is important for the evolution of new biosynthetic pathways.^[25]

"Lock and key" model

Enzymes are very specific, and it was suggested by Emil Fischer in 1894 that this was because both the enzyme and the substrate possess specific complementary geometric shapes that fit exactly into one another.^[26] This is often referred to as "the lock and key" model. However, while this model explains enzyme specificity, it fails to explain the stabilization of the transition state that enzymes achieve. The "lock and key" model has proven inaccurate, and the induced fit model is the most currently accepted enzyme-substrate-coenzyme figure.

Induced fit model

Diagrams to show the induced fit hypothesis of enzyme action.

In 1958, Daniel Koshland suggested a modification to the lock and key model: since enzymes are rather flexible structures, the active site is continually reshaped by interactions with the substrate as the substrate interacts with the enzyme.^[27] As a result, the substrate does not simply bind to a rigid active site; the amino acid side chains which make up the active site are molded into the precise positions that enable the enzyme to perform its catalytic function. In some cases, such as glycosidases, the substrate molecule also changes shape slightly as it enters the active site.^[28] The active site continues to change until the substrate is completely bound, at which point the final shape and charge is determined.^[29]

Mechanisms

Enzymes can act in several ways, all of which lower ΔG^‡:^[30]

• Lowering the activation energy by creating an environment in which the transition state is stabilized (e.g. straining the shape of a substrate—by binding the transition-state conformation of the substrate/product molecules, the enzyme distorts the bound substrate(s) into their transition state form, thereby reducing the amount of energy required to complete the transition).
• Lowering the energy of the transition state, but without distorting the substrate, by creating an environment with the opposite charge distribution to that of the transition state.
• Providing an alternative pathway. For example, temporarily reacting with the substrate to form an intermediate ES complex, which would be impossible in the absence of the enzyme.
• Reducing the reaction entropy change by bringing substrates together in the correct orientation to react. Considering ΔH^‡ alone overlooks this effect.
• Increases in temperatures speed up reactions. Thus, temperature increases help the enzyme function and develop the end product even faster. However, if heated too much, the enzyme’s shape deteriorates and only when the temperature comes back to normal does the enzyme regain its shape. Some enzymes like thermolabile enzymes work best at low temperatures.

Interestingly, this entropic effect involves destabilization of the ground state,^[31] and its contribution to catalysis is relatively small.^[32]

Transition State Stabilization

The understanding of the origin of the reduction of ΔG^‡ requires one to find out how the enzymes can stabilize its transition state more than the transition state of the uncatalyzed reaction. Apparently, the most effective way for reaching large stabilization is the use of electrostatic effects, in particular, by having a relatively fixed polar environment that is oriented toward the charge distribution of the transition state.^[33] Such an environment does not exist in the uncatalyzed reaction in water.

Dynamics and function

See also: Protein dynamics

The internal dynamics of enzymes is connected to their mechanism of catalysis.^[34][35][36] Internal dynamics are the movement of parts of the enzyme's structure, such as individual amino acid residues, a group of amino acids, or even an entire protein domain. These movements occur at various time-scales ranging from femtoseconds to seconds. Networks of protein residues throughout an enzyme's structure can contribute to catalysis through dynamic motions.^{[37][38][39][40]} Protein motions are vital to many enzymes, but whether small and fast vibrations, or larger and slower conformational movements are more important depends on the type of reaction involved. However, although these movements are important in binding and releasing substrates and products, it is not clear if protein movements help to accelerate the chemical steps in enzymatic reactions.^[41] These new insights also have implications in understanding allosteric effects and developing new drugs.

Allosteric modulation

Allosteric sites are pouches on the enzyme that attract molecules drifting about in the cellular environment. They form weak, noncovalent bonds with these molecules, causing a change in the conformation of the enzyme. This change in conformation translates to the active site, which then affects the reaction rate of the enzyme. Allosteric modulation is both an inhibitor and an activator.

Cofactors and coenzymes

Main articles: Cofactor (biochemistry) and Coenzyme

Cofactors

Some enzymes do not need any additional components to show full activity. However, others require non-protein molecules called cofactors to be bound for activity.^[42] Cofactors can be either inorganic (e.g., metal ions and iron-sulfur clusters) or organic compounds (e.g., flavin and heme). Organic cofactors can be either prosthetic groups, which are tightly bound to an enzyme, or coenzymes, which are released from the enzyme's active site during the reaction. Coenzymes include NADH, NADPH and adenosine triphosphate. These molecules transfer chemical groups between enzymes.^[43]

An example of an enzyme that contains a cofactor is carbonic anhydrase, and is shown in the ribbon diagram above with a zinc cofactor bound as part of its active site.^[44] These tightly bound molecules are usually found in the active site and are involved in catalysis. For example, flavin and heme cofactors are often involved in redox reactions.

Enzymes that require a cofactor but do not have one bound are called apoenzymes or apoproteins. An apoenzyme together with its cofactor(s) is called a holoenzyme (this is the active form). Most cofactors are not covalently attached to an enzyme, but are very tightly bound. However, organic prosthetic groups can be covalently bound (e.g., thiamine pyrophosphate in the enzyme pyruvate dehydrogenase). The term "holoenzyme" can also be applied to enzymes that contain multiple protein subunits, such as the DNA polymerases; here the holoenzyme is the complete complex containing all the subunits needed for activity.

Coenzymes

Space-filling model of the coenzyme NADH

Coenzymes are small organic molecules that transport chemical groups from one enzyme to another.^[45] Some of these chemicals such as riboflavin, thiamine and folic acid are vitamins (compounds which cannot be synthesized by the body and must be acquired from the diet). The chemical groups carried include the hydride ion (H^-) carried by NAD or NADP⁺, the acetyl group carried by coenzyme A, formyl, methenyl or methyl groups carried by folic acid and the methyl group carried by S-adenosylmethionine.

Since coenzymes are chemically changed as a consequence of enzyme action, it is useful to consider coenzymes to be a special class of substrates, or second substrates, which are common to many different enzymes. For example, about 700 enzymes are known to use the coenzyme NADH.^[46]

Coenzymes are usually regenerated and their concentrations maintained at a steady level inside the cell: for example, NADPH is regenerated through the pentose phosphate pathway and S-adenosylmethionine by methionine adenosyltransfera Co enzymes are involved in the transfer of hydrogen ions and electrons

Thermodynamics

The energies of the stages of a chemical reaction. Substrates need a lot of energy to reach a transition state, which then decays into products. The enzyme stabilizes the transition state, reducing the energy needed to form products.

Main articles: Activation energy, Thermodynamic equilibrium, and Chemical equilibrium

As all catalysts, enzymes do not alter the position of the chemical equilibrium of the reaction. Usually, in the presence of an enzyme, the reaction runs in the same direction as it would without the enzyme, just more quickly. However, in the absence of the enzyme, other possible uncatalyzed, "spontaneous" reactions might lead to different products, because in those conditions this different product is formed faster.

Furthermore, enzymes can couple two or more reactions, so that a thermodynamically favorable reaction can be used to "drive" a thermodynamically unfavorable one. For example, the hydrolysis of ATP is often used to drive other chemical reactions.

Enzymes catalyze the forward and backward reactions equally. They do not alter the equilibrium itself, but only the speed at which it is reached. For example, carbonic anhydrase catalyzes its reaction in either direction depending on the concentration of its reactants.

(in tissues; high CO₂ concentration)

(in lungs; low CO₂ concentration)

Nevertheless, if the equilibrium is greatly displaced in one direction, that is, in a very exergonic reaction, the reaction is effectively irreversible. Under these conditions the enzyme will, in fact, only catalyze the reaction in the thermodynamically allowed direction.

Kinetics

Main article: Enzyme kinetics

Mechanism for a single substrate enzyme catalyzed reaction. The enzyme (E) binds a substrate (S) and produces a product (P).

Enzyme kinetics is the investigation of how enzymes bind substrates and turn them into products. The rate data used in kinetic analyses are obtained from enzyme assays.

In 1902 Victor Henri^[47] proposed a quantitative theory of enzyme kinetics, but his experimental data were not useful because the significance of the hydrogen ion concentration was not yet appreciated. After Peter Lauritz Sørensen had defined the logarithmic pH-scale and introduced the concept of buffering in 1909^[48] the German chemist Leonor Michaelis and his Canadian postdoc Maud Leonora Menten repeated Henri's experiments and confirmed his equation which is referred to as Henri-Michaelis-Menten kinetics (sometimes also Michaelis-Menten kinetics).^[49] Their work was further developed by G. E. Briggs and J. B. S. Haldane, who derived kinetic equations that are still widely used today.^[50]

The major contribution of Henri was to think of enzyme reactions in two stages. In the first, the substrate binds reversibly to the enzyme, forming the enzyme-substrate complex. This is sometimes called the Michaelis complex. The enzyme then catalyzes the chemical step in the reaction and releases the product.

Saturation curve for an enzyme reaction showing the relation between the substrate concentration (S) and rate (v).

Enzymes can catalyze up to several million reactions per second. For example, the uncatalyzed decarboxylation of orotidine 5'-monophosphate has a half life of 78 million years. However, when the enzyme orotidine 5'-phosphate decarboxylase is added, the same process takes just 25 milliseconds.^[51] Enzyme rates depend on solution conditions and substrate concentration. Conditions that denature the protein abolish enzyme activity, such as high temperatures, extremes of pH or high salt concentrations, while raising substrate concentration tends to increase activity. To find the maximum speed of an enzymatic reaction, the substrate concentration is increased until a constant rate of product formation is seen. This is shown in the saturation curve on the right. Saturation happens because, as substrate concentration increases, more and more of the free enzyme is converted into the substrate-bound ES form. At the maximum velocity (V_max) of the enzyme, all the enzyme active sites are bound to substrate, and the amount of ES complex is the same as the total amount of enzyme. However, V_max is only one kinetic constant of enzymes. The amount of substrate needed to achieve a given rate of reaction is also important. This is given by the Michaelis-Menten constant (K_m), which is the substrate concentration required for an enzyme to reach one-half its maximum velocity. Each enzyme has a characteristic K_m for a given substrate, and this can show how tight the binding of the substrate is to the enzyme. Another useful constant is k_cat, which is the number of substrate molecules handled by one active site per second.

The efficiency of an enzyme can be expressed in terms of k_cat/K_m. This is also called the specificity constant and incorporates the rate constants for all steps in the reaction. Because the specificity constant reflects both affinity and catalytic ability, it is useful for comparing different enzymes against each other, or the same enzyme with different substrates. The theoretical maximum for the specificity constant is called the diffusion limit and is about 10⁸ to 10⁹ (M^-1 s^-1). At this point every collision of the enzyme with its substrate will result in catalysis, and the rate of product formation is not limited by the reaction rate but by the diffusion rate. Enzymes with this property are called catalytically perfect or kinetically perfect. Example of such enzymes are triose-phosphate isomerase, carbonic anhydrase, acetylcholinesterase, catalase, fumarase, β-lactamase, and superoxide dismutase.

Michaelis-Menten kinetics relies on the law of mass action, which is derived from the assumptions of free diffusion and thermodynamically driven random collision. However, many biochemical or cellular processes deviate significantly from these conditions, because of macromolecular crowding, phase-separation of the enzyme/substrate/product, or one or two-dimensional molecular movement.^[52] In these situations, a fractal Michaelis-Menten kinetics may be applied.^{[53][54][55][56]}

Some enzymes operate with kinetics which are faster than diffusion rates, which would seem to be impossible. Several mechanisms have been invoked to explain this phenomenon. Some proteins are believed to accelerate catalysis by drawing their substrate in and pre-orienting them by using dipolar electric fields. Other models invoke a quantum-mechanical tunneling explanation, whereby a proton or an electron can tunnel through activation barriers, although for proton tunneling this model remains somewhat controversial.^[57][58] Quantum tunneling for protons has been observed in tryptamine.^[59] This suggests that enzyme catalysis may be more accurately characterized as "through the barrier" rather than the traditional model, which requires substrates to go "over" a lowered energy barrier.

Inhibition

Competitive inhibitors bind reversibly to the enzyme, preventing the binding of substrate. On the other hand, binding of substrate prevents binding of the inhibitor. Substrate and inhibitor compete for the enzyme.

Types of inhibition. This classification was introduced by W.W. Cleland.^[60]

Main article: Enzyme inhibitor

Enzyme reaction rates can be decreased by various types of enzyme inhibitors.

Competitive inhibition

In competitive inhibition, the inhibitor and substrate compete for the enzyme (i.e., they can not bind at the same time).^[61] Often competitive inhibitors strongly resemble the real substrate of the enzyme. For example, methotrexate is a competitive inhibitor of the enzyme dihydrofolate reductase, which catalyzes the reduction of dihydrofolate to tetrahydrofolate. The similarity between the structures of folic acid and this drug are shown in the figure to the right bottom. Note that binding of the inhibitor need not be to the substrate binding site (as frequently stated), if binding of the inhibitor changes the conformation of the enzyme to prevent substrate binding and vice versa. In competitive inhibition the maximal velocity of the reaction is not changed, but higher substrate concentrations are required to reach a given velocity, increasing the apparent K_m.

Uncompetitive inhibition

In uncompetitive inhibition the inhibitor can not bind to the free enzyme, but only to the ES-complex. The EIS-complex thus formed is enzymatically inactive. This type of inhibition is rare, but may occur in multimeric enzymes.

Non-competitive inhibition

Non-competitive inhibitors can bind to the enzyme at the same time as the substrate, i.e. they never bind to the active site. Both the EI and EIS complexes are enzymatically inactive. Because the inhibitor can not be driven from the enzyme by higher substrate concentration (in contrast to competitive inhibition), the apparent V_max changes. But because the substrate can still bind to the enzyme, the K_m stays the same.

Mixed inhibition

This type of inhibition resembles the non-competitive, except that the EIS-complex has residual enzymatic activity.

In many organisms inhibitors may act as part of a feedback mechanism. If an enzyme produces too much of one substance in the organism, that substance may act as an inhibitor for the enzyme at the beginning of the pathway that produces it, causing production of the substance to slow down or stop when there is sufficient amount. This is a form of negative feedback. Enzymes which are subject to this form of regulation are often multimeric and have allosteric binding sites for regulatory substances. Their substrate/velocity plots are not hyperbolar, but sigmoidal (S-shaped).

The coenzyme folic acid (left) and the anti-cancer drug methotrexate (right) are very similar in structure. As a result, methotrexate is a competitive inhibitor of many enzymes that use folates.

Irreversible inhibitors react with the enzyme and form a covalent adduct with the protein. The inactivation is irreversible. These compounds include eflornithine a drug used to treat the parasitic disease sleeping sickness.^[62] Penicillin and Aspirin also act in this manner. With these drugs, the compound is bound in the active site and the enzyme then converts the inhibitor into an activated form that reacts irreversibly with one or more amino acid residues.

Uses of inhibitors

Since inhibitors modulate the function of enzymes they are often used as drugs. An common example of an inhibitor that is used as a drug is aspirin, which inhibits the COX-1 and COX-2 enzymes that produce the inflammation messenger prostaglandin, thus suppressing pain and inflammation. However, other enzyme inhibitors are poisons. For example, the poison cyanide is an irreversible enzyme inhibitor that combines with the copper and iron in the active site of the enzyme cytochrome c oxidase and blocks cellular respiration.^[63]

Biological function

Enzymes serve a wide variety of functions inside living organisms. They are indispensable for signal transduction and cell regulation, often via kinases and phosphatases.^[64] They also generate movement, with myosin hydrolysing ATP to generate muscle contraction and also moving cargo around the cell as part of the cytoskeleton.^[65] Other ATPases in the cell membrane are ion pumps involved in active transport. Enzymes are also involved in more exotic functions, such as luciferase generating light in fireflies.^[66] Viruses can also contain enzymes for infecting cells, such as the HIV integrase and reverse transcriptase, or for viral release from cells, like the influenza virus neuraminidase.

An important function of enzymes is in the digestive systems of animals. Enzymes such as amylases and proteases break down large molecules (starch or proteins, respectively) into smaller ones, so they can be absorbed by the intestines. Starch molecules, for example, are too large to be absorbed from the intestine, but enzymes hydrolyse the starch chains into smaller molecules such as maltose and eventually glucose, which can then be absorbed. Different enzymes digest different food substances. In ruminants which have herbivorous diets, microorganisms in the gut produce another enzyme, cellulase to break down the cellulose cell walls of plant fiber.^[67]

Several enzymes can work together in a specific order, creating metabolic pathways. In a metabolic pathway, one enzyme takes the product of another enzyme as a substrate. After the catalytic reaction, the product is then passed on to another enzyme. Sometimes more than one enzyme can catalyze the same reaction in parallel, this can allow more complex regulation: with for example a low constant activity being provided by one enzyme but an inducible high activity from a second enzyme.

Enzymes determine what steps occur in these pathways. Without enzymes, metabolism would neither progress through the same steps, nor be fast enough to serve the needs of the cell. Indeed, a metabolic pathway such as glycolysis could not exist independently of enzymes. Glucose, for example, can react directly with ATP to become phosphorylated at one or more of its carbons. In the absence of enzymes, this occurs so slowly as to be insignificant. However, if hexokinase is added, these slow reactions continue to take place except that phosphorylation at carbon 6 occurs so rapidly that if the mixture is tested a short time later, glucose-6-phosphate is found to be the only significant product. Consequently, the network of metabolic pathways within each cell depends on the set of functional enzymes that are present.

Control of activity

There are five main ways that enzyme activity is controlled in the cell.

1. Enzyme production (transcription and translation of enzyme genes) can be enhanced or diminished by a cell in response to changes in the cell's environment. This form of gene regulation is called enzyme induction and inhibition (see enzyme induction). For example, bacteria may become resistant to antibiotics such as penicillin because enzymes called beta-lactamases are induced that hydrolyse the crucial beta-lactam ring within the penicillin molecule. Another example are enzymes in the liver called cytochrome P450 oxidases, which are important in drug metabolism. Induction or inhibition of these enzymes can cause drug interactions.
2. Enzymes can be compartmentalized, with different metabolic pathways occurring in different cellular compartments. For example, fatty acids are synthesized by one set of enzymes in the cytosol, endoplasmic reticulum and the Golgi apparatus and used by a different set of enzymes as a source of energy in the mitochondrion, through β-oxidation.^[68]
3. Enzymes can be regulated by inhibitors and activators. For example, the end product(s) of a metabolic pathway are often inhibitors for one of the first enzymes of the pathway (usually the first irreversible step, called committed step), thus regulating the amount of end product made by the pathways. Such a regulatory mechanism is called a negative feedback mechanism, because the amount of the end product produced is regulated by its own concentration. Negative feedback mechanism can effectively adjust the rate of synthesis of intermediate metabolites according to the demands of the cells. This helps allocate materials and energy economically, and prevents the manufacture of excess end products. The control of enzymatic action helps to maintain a stable internal environment in living organisms.
4. Enzymes can be regulated through post-translational modification. This can include phosphorylation, myristoylation and glycosylation. For example, in the response to insulin, the phosphorylation of multiple enzymes, including glycogen synthase, helps control the synthesis or degradation of glycogen and allows the cell to respond to changes in blood sugar.^[69] Another example of post-translational modification is the cleavage of the polypeptide chain. Chymotrypsin, a digestive protease, is produced in inactive form as chymotrypsinogen in the pancreas and transported in this form to the stomach where it is activated. This stops the enzyme from digesting the pancreas or other tissues before it enters the gut. This type of inactive precursor to an enzyme is known as a zymogen.
5. Some enzymes may become activated when localized to a different environment (eg. from a reducing (cytoplasm) to an oxidising (periplasm) environment, high pH to low pH etc). For example, hemagglutinin in the influenza virus is activated by a conformational change caused by the acidic conditions, these occur when it is taken up inside its host cell and enters the lysosome.^[70]

Involvement in disease

Phenylalanine hydroxylase. Created from PDB 1KW0

Since the tight control of enzyme activity is essential for homeostasis, any malfunction (mutation, overproduction, underproduction or deletion) of a single critical enzyme can lead to a genetic disease. The importance of enzymes is shown by the fact that a lethal illness can be caused by the malfunction of just one type of enzyme out of the thousands of types present in our bodies.

One example is the most common type of phenylketonuria. A mutation of a single amino acid in the enzyme phenylalanine hydroxylase, which catalyzes the first step in the degradation of phenylalanine, results in build-up of phenylalanine and related products. This can lead to mental retardation if the disease is untreated.^[71]

Another example is when germline mutations in genes coding for DNA repair enzymes cause hereditary cancer syndromes such as xeroderma pigmentosum. Defects in these enzymes cause cancer since the body is less able to repair mutations in the genome. This causes a slow accumulation of mutations and results in the development of many types of cancer in the sufferer.

Naming conventions

An enzyme's name is often derived from its substrate or the chemical reaction it catalyzes, with the word ending in -ase. Examples are lactase, alcohol dehydrogenase and DNA polymerase. This may result in different enzymes, called isozymes, with the same function having the same basic name. Isoenzymes have a different amino acid sequence and might be distinguished by their optimal pH, kinetic properties or immunologically. Furthermore, the normal physiological reaction an enzyme catalyzes may not be the same as under artificial conditions. This can result in the same enzyme being identified with two different names. E.g. Glucose isomerase, used industrially to convert glucose into the sweetener fructose, is a xylose isomerase in vivo.

The International Union of Biochemistry and Molecular Biology have developed a nomenclature for enzymes, the EC numbers; each enzyme is described by a sequence of four numbers preceded by "EC". The first number broadly classifies the enzyme based on its mechanism.

The top-level classification is

• EC 1 Oxidoreductases: catalyze oxidation/reduction reactions
• EC 2 Transferases: transfer a functional group (e.g. a methyl or phosphate group)
• EC 3 Hydrolases: catalyze the hydrolysis of various bonds
• EC 4 Lyases: cleave various bonds by means other than hydrolysis and oxidation
• EC 5 Isomerases: catalyze isomerization changes within a single molecule
• EC 6 Ligases: join two molecules with covalent bonds.

The complete nomenclature can be browsed at http://www.chem.qmul.ac.uk/iubmb/enzyme/.

Industrial applications

Enzymes are used in the chemical industry and other industrial applications when extremely specific catalysts are required. However, enzymes in general are limited in the number of reactions they have evolved to catalyze and also by their lack of stability in organic solvents and at high temperatures. Consequently, protein engineering is an active area of research and involves attempts to create new enzymes with novel properties, either through rational design or in vitro evolution.^[72][73] These efforts have begun to be successful, and a few enzymes have now been desiged "from scratch" to catalyse reactions that do not occur in nature.^[74]

Application	Enzymes used	Uses
Food processing Amylases catalyze the release of simple sugars from starch	Amylases from fungi and plants.	Production of sugars from starch, such as in making high-fructose corn syrup.[75] In baking, catalyze breakdown of starch in the flour to sugar. Yeast fermentation of sugar produces the carbon dioxide that raises the dough.
	Proteases	Biscuit manufacturers use them to lower the protein level of flour.
Baby foods	Trypsin	To predigest baby foods.
Brewing industry Germinating barley used for malt.	Enzymes from barley are released during the mashing stage of beer production.	They degrade starch and proteins to produce simple sugar, amino acids and peptides that are used by yeast for fermentation.
	Industrially produced barley enzymes	Widely used in the brewing process to substitute for the natural enzymes found in barley.
	Amylase, glucanases, proteases	Split polysaccharides and proteins in the malt.
	Betaglucanases and arabinoxylanases	Improve the wort and beer filtration characteristics.
	Amyloglucosidase and pullulanases	Low-calorie beer and adjustment of fermentability.
	Proteases	Remove cloudiness produced during storage of beers.
	Acetolactatedecarboxylase (ALDC)	Increases fermentation efficiency by reducing diacetyl formation.[76]
Fruit juices	Cellulases, pectinases	Clarify fruit juices
Dairy industry Roquefort cheese	Rennin, derived from the stomachs of young ruminant animals (like calves and lambs).	Manufacture of cheese, used to hydrolyze protein.
	Microbially produced enzyme	Now finding increasing use in the dairy industry.
	Lipases	Is implemented during the production of Roquefort cheese to enhance the ripening of the blue-mould cheese.
	Lactases	Break down lactose to glucose and galactose.
Meat tenderizers	Papain	To soften meat for cooking.
Starch industry Glucose Fructose	Amylases, amyloglucosideases and glucoamylases	Converts starch into glucose and various syrups.
	Glucose isomerase	Converts glucose into fructose in production of high fructose syrups from starchy materials. These syrups have enhanced sweetening properties and lower calorific values than sucrose for the same level of sweetness.
Paper industry A paper mill in South Carolina.	Amylases, Xylanases, Cellulases and ligninases	Degrade starch to lower viscosity, aiding sizing and coating paper. Xylanases reduce bleach required for decolorising; cellulases smooth fibers, enhance water drainage, and promote ink removal; lipases reduce pitch and lignin-degrading enzymes remove lignin to soften paper.
Biofuel industry Cellulose in 3D	Cellulases	Used to break down cellulose into sugars that can be fermented (see cellulosic ethanol).
	Ligninases	Use of lignin waste
Biological detergent	Primarily proteases, produced in an extracellular form from bacteria	Used for presoak conditions and direct liquid applications helping with removal of protein stains from clothes.
	Amylases	Detergents for machine dish washing to remove resistant starch residues.
	Lipases	Used to assist in the removal of fatty and oily stains.
	Cellulases	Used in biological fabric conditioners.
Contact lens cleaners	Proteases	To remove proteins on contact lens to prevent infections.
Rubber industry	Catalase	To generate oxygen from peroxide to convert latex into foam rubber.
Photographic industry	Protease (ficin)	Dissolve gelatin off scrap film, allowing recovery of its silver content.
Molecular biology Part of the DNA double helix.	Restriction enzymes, DNA ligase and polymerases	Used to manipulate DNA in genetic engineering, important in pharmacology, agriculture and medicine. Essential for restriction digestion and the polymerase chain reaction. Molecular biology is also important in forensic science.

See also

Food portal

• List of enzymes
• Enzyme product
• Enzyme substrate
• Enzyme catalysis
• Protein dynamics
• The Proteolysis Map
• RNA Biocatalysis
• SUMO enzymes
• K_i Database
• Proteonomics and protein engineering
• Immobilized enzyme
• Kinetic Perfection
• Enzyme engineering

References

1. ^ Smith AL (Ed) et al. (1997). Oxford dictionary of biochemistry and molecular biology. Oxford [Oxfordshire]: Oxford University Press. ISBN 0-19-854768-4. 
2. ^ Grisham, Charles M.; Reginald H. Garrett (1999). Biochemistry. Philadelphia: Saunders College Pub. pp. 426–7. ISBN 0-03-022318-0. 
3. ^ Bairoch A. (2000). "The ENZYME database in 2000" (PDF). Nucleic Acids Res 28 (1): 304–5. doi:10.1093/nar/28.1.304. PMID 10592255. PMC 102465. http://www.expasy.org/NAR/enz00.pdf. 
4. ^ Lilley D (2005). "Structure, folding and mechanisms of ribozymes". Curr Opin Struct Biol 15 (3): 313–23. doi:10.1016/j.sbi.2005.05.002. PMID 15919196. 
5. ^ Cech T (2000). "Structural biology. The ribosome is a ribozyme". Science 289 (5481): 878–9. doi:10.1126/science.289.5481.878. PMID 10960319. 
6. ^ Groves JT (1997). "Artificial enzymes. The importance of being selective". Nature 389 (6649): 329–30. doi:10.1038/38602. PMID 9311771. 
7. ^ de Réaumur, RAF (1752). "Observations sur la digestion des oiseaux". Histoire de l'academie royale des sciences 1752: 266, 461. 
8. ^ Williams, H. S. (1904) A History of Science: in Five Volumes. Volume IV: Modern Development of the Chemical and Biological Sciences Harper and Brothers (New York) Accessed 4 April 2007
9. ^ Dubos J. (1951). "Louis Pasteur: Free Lance of Science, Gollancz. Quoted in Manchester K. L. (1995) Louis Pasteur (1822–1895)—chance and the prepared mind". Trends Biotechnol 13 (12): 511–5. doi:10.1016/S0167-7799(00)89014-9. PMID 8595136. 
10. ^ Nobel Laureate Biography of Eduard Buchner at http://nobelprize.org. Retrieved 4 April 2007.
11. ^ Text of Eduard Buchner's 1907 Nobel lecture at http://nobelprize.org. Retrieved 4 April 2007.
12. ^ 1946 Nobel prize for Chemistry laureates at http://nobelprize.org. Retrieved 4 April 2007.
13. ^ Blake CC, Koenig DF, Mair GA, North AC, Phillips DC, Sarma VR. (1965). "Structure of hen egg-white lysozyme. A three-dimensional Fourier synthesis at 2 Angstrom resolution". Nature 22 (206): 757–61. doi:10.1038/206757a0. PMID 5891407. 
14. ^ Chen LH, Kenyon GL, Curtin F, Harayama S, Bembenek ME, Hajipour G, Whitman CP (1992). "4-Oxalocrotonate tautomerase, an enzyme composed of 62 amino acid residues per monomer". J. Biol. Chem. 267 (25): 17716–21. PMID 1339435. 
15. ^ Smith S (1 December 1994). "The animal fatty acid synthase: one gene, one polypeptide, seven enzymes". FASEB J. 8 (15): 1248–59. PMID 8001737. http://www.fasebj.org/cgi/reprint/8/15/1248. 
16. ^ Anfinsen C.B. (1973). "Principles that Govern the Folding of Protein Chains". Science 181 (96): 223–30. doi:10.1126/science.181.4096.223. PMID 4124164. 
17. ^ Dunaway-Mariano D (November 2008). "Enzyme function discovery". Structure 16 (11): 1599–600. doi:10.1016/j.str.2008.10.001. PMID 19000810. 
18. ^ The Catalytic Site Atlas at The European Bioinformatics Institute. Retrieved 4 April 2007.
19. ^ Jaeger KE, Eggert T. (2004). "Enantioselective biocatalysis optimized by directed evolution". Curr Opin Biotechnol. 15 (4): 305–13. doi:10.1016/j.copbio.2004.06.007. PMID 15358000. 
20. ^ Shevelev IV, Hubscher U. (2002). "The 3' 5' exonucleases". Nat Rev Mol Cell Biol. 3 (5): 364–76. doi:10.1038/nrm804. PMID 11988770. 
21. ^ Tymoczko, John L.; Stryer Berg Tymoczko; Stryer, Lubert; Berg, Jeremy Mark (2002). Biochemistry. San Francisco: W.H. Freeman. ISBN 0-7167-4955-6. 
22. ^ Zenkin N, Yuzenkova Y, Severinov K. (2006). "Transcript-assisted transcriptional proofreading". Science. 313 (5786): 518–20. doi:10.1126/science.1127422. PMID 16873663. 
23. ^ Ibba M, Soll D. (2000). "Aminoacyl-tRNA synthesis". Annu Rev Biochem. 69: 617–50. doi:10.1146/annurev.biochem.69.1.617. PMID 10966471. 
24. ^ Rodnina MV, Wintermeyer W. (2001). "Fidelity of aminoacyl-tRNA selection on the ribosome: kinetic and structural mechanisms". Annu Rev Biochem. 70: 415–35. doi:10.1146/annurev.biochem.70.1.415. PMID 11395413. 
25. ^ Firn, Richard. "The Screening Hypothesis - a new explanation of secondary product diversity and function". http://www-users.york.ac.uk/~drf1/rdf_sp1.htm. Retrieved 2006-10-11. 
26. ^ Fischer E. (1894). "Einfluss der Configuration auf die Wirkung der Enzyme". Ber. Dt. Chem. Ges. 27: 2985–93. doi:10.1002/cber.18940270364. http://gallica.bnf.fr/ark:/12148/bpt6k90736r/f364.chemindefer. 
27. ^ Koshland D. E. (1958). "Application of a Theory of Enzyme Specificity to Protein Synthesis". Proc. Natl. Acad. Sci. 44 (2): 98–104. doi:10.1073/pnas.44.2.98. PMID 16590179. 
28. ^ Vasella A, Davies GJ, Bohm M. (2002). "Glycosidase mechanisms". Curr Opin Chem Biol. 6 (5): 619–29. doi:10.1016/S1367-5931(02)00380-0. PMID 12413546. 
29. ^ Boyer, Rodney (2002) [2002]. "6". Concepts in Biochemistry (2nd ed.). New York, Chichester, Weinheim, Brisbane, Singapore, Toronto.: John Wiley & Sons, Inc.. pp. 137–8. ISBN 0-470-00379-0. OCLC 51720783. 
30. ^ Fersht, Alan (1985). Enzyme structure and mechanism. San Francisco: W.H. Freeman. pp. 50–2. ISBN 0-7167-1615-1. 
31. ^ Jencks, William P. (1987). Catalysis in chemistry and enzymology. Mineola, N.Y: Dover. ISBN 0-486-65460-5. 
32. ^ Villa J, Strajbl M, Glennon TM, Sham YY, Chu ZT, Warshel A (2000). "How important are entropic contributions to enzyme catalysis?". Proc. Natl. Acad. Sci. U.S.A. 97 (22): 11899–904. doi:10.1073/pnas.97.22.11899. PMID 11050223. 
33. ^ Warshel A, Sharma PK, Kato M, Xiang Y, Liu H, Olsson MH (2006). "Electrostatic basis for enzyme catalysis". Chem. Rev. 106 (8): 3210–35. doi:10.1021/cr0503106. PMID 16895325. 
34. ^ Eisenmesser EZ, Bosco DA, Akke M, Kern D (February 2002). "Enzyme dynamics during catalysis". Science 295 (5559): 1520–3. doi:10.1126/science.1066176. PMID 11859194. 
35. ^ Agarwal PK (November 2005). "Role of protein dynamics in reaction rate enhancement by enzymes". J. Am. Chem. Soc. 127 (43): 15248–56. doi:10.1021/ja055251s. PMID 16248667. 
36. ^ Eisenmesser EZ, Millet O, Labeikovsky W (November 2005). "Intrinsic dynamics of an enzyme underlies catalysis". Nature 438 (7064): 117–21. doi:10.1038/nature04105. PMID 16267559. 
37. ^ Yang LW, Bahar I (5 June 2005). "Coupling between catalytic site and collective dynamics: A requirement for mechanochemical activity of enzymes". Structure 13 (6): 893–904. doi:10.1016/j.str.2005.03.015. PMID 15939021. PMC 1489920. http://www.cell.com/structure/abstract/S0969-2126%2805%2900167-X. 
38. ^ Agarwal PK, Billeter SR, Rajagopalan PT, Benkovic SJ, Hammes-Schiffer S. (5 March 2002). "Network of coupled promoting motions in enzyme catalysis". Proc Natl Acad Sci USA. 99 (5): 2794–9. doi:10.1073/pnas.052005999. PMID 11867722. 
39. ^ Agarwal PK, Geist A, Gorin A (August 2004). "Protein dynamics and enzymatic catalysis: investigating the peptidyl-prolyl cis-trans isomerization activity of cyclophilin A". Biochemistry 43 (33): 10605–18. doi:10.1021/bi0495228. PMID 15311922. 
40. ^ Tousignant A, Pelletier JN. (August 2004). "Protein motions promote catalysis". Chem Biol. 11 (8): 1037–42. doi:10.1016/j.chembiol.2004.06.007. PMID 15324804. http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRP-4D4JYMC-6&_coverDate=08%2F31%2F2004&_alid=465962916&_rdoc=1&_fmt=&_orig=search&_qd=1&_cdi=6240&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=613585a6164baa38b4f6536d8da9170a. 
41. ^ Olsson, MH; Parson, WW; Warshel, A (2006). "Dynamical Contributions to Enzyme Catalysis: Critical Tests of A Popular Hypothesis". Chem. Rev. 106 (5): 1737–56. doi:10.1021/cr040427e. PMID 16683752. 
42. ^ de Bolster, M.W.G. (1997). "Glossary of Terms Used in Bioinorganic Chemistry: Cofactor". International Union of Pure and Applied Chemistry. http://www.chem.qmul.ac.uk/iupac/bioinorg/CD.html#34. Retrieved 2007-10-30. 
43. ^ de Bolster, M.W.G. (1997). "Glossary of Terms Used in Bioinorganic Chemistry: Coenzyme". International Union of Pure and Applied Chemistry. http://www.chem.qmul.ac.uk/iupac/bioinorg/CD.html#33. Retrieved 2007-10-30. 
44. ^ Fisher Z, Hernandez Prada JA, Tu C, Duda D, Yoshioka C, An H, Govindasamy L, Silverman DN and McKenna R. (2005). "Structural and kinetic characterization of active-site histidine as a proton shuttle in catalysis by human carbonic anhydrase II". Biochemistry. 44 (4): 1097–115. doi:10.1021/bi0480279. PMID 15667203. 
45. ^ Wagner, Arthur L. (1975). Vitamins and Coenzymes. Krieger Pub Co. ISBN 0-88275-258-8. 
46. ^ BRENDA The Comprehensive Enzyme Information System. Retrieved 4 April 2007.
47. ^ Henri, V. (1902). "Theorie generale de l'action de quelques diastases". Compt. Rend. Hebd. Acad. Sci. Paris 135: 916–9. 
48. ^ Sørensen,P.L. (1909). "Enzymstudien {II}. Über die Messung und Bedeutung der Wasserstoffionenkonzentration bei enzymatischen Prozessen". Biochem. Z. 21: 131–304. 
49. ^ Michaelis L., Menten M. (1913). "Die Kinetik der Invertinwirkung". Biochem. Z. 49: 333–369.  English translation. Retrieved 6 April 2007.
50. ^ Briggs G. E., Haldane J. B. S. (1925). "A note on the kinetics of enzyme action". Biochem. J. 19 (2): 339–339. PMID 16743508. PMC 1259181. http://www.biochemj.org/bj/019/0338/bj0190338_browse.htm. 
51. ^ Radzicka A, Wolfenden R. (1995). "A proficient enzyme". Science 6 (267): 90–931. doi:10.1126/science.7809611. PMID 7809611. 
52. ^ Ellis RJ (2001). "Macromolecular crowding: obvious but underappreciated". Trends Biochem. Sci. 26 (10): 597–604. doi:10.1016/S0968-0004(01)01938-7. PMID 11590012. 
53. ^ Kopelman R (1988). "Fractal Reaction Kinetics". Science 241 (4873): 1620–26. doi:10.1126/science.241.4873.1620. PMID 17820893. 
54. ^ Savageau MA (1995). "Michaelis-Menten mechanism reconsidered: implications of fractal kinetics". J. Theor. Biol. 176 (1): 115–24. doi:10.1006/jtbi.1995.0181. PMID 7475096. 
55. ^ Schnell S, Turner TE (2004). "Reaction kinetics in intracellular environments with macromolecular crowding: simulations and rate laws". Prog. Biophys. Mol. Biol. 85 (2–3): 235–60. doi:10.1016/j.pbiomolbio.2004.01.012. PMID 15142746. 
56. ^ Xu F, Ding H (2007). "A new kinetic model for heterogeneous (or spatially confined) enzymatic catalysis: Contributions from the fractal and jamming (overcrowding) effects". Appl. Catal. A: Gen. 317 (1): 70–81. doi:10.1016/j.apcata.2006.10.014. 
57. ^ Garcia-Viloca M., Gao J., Karplus M., Truhlar D. G. (2004). "How enzymes work: analysis by modern rate theory and computer simulations". Science 303 (5655): 186–95. doi:10.1126/science.1088172. PMID 14716003. 
58. ^ Olsson M. H., Siegbahn P. E., Warshel A. (2004). "Simulations of the large kinetic isotope effect and the temperature dependence of the hydrogen atom transfer in lipoxygenase". J. Am. Chem. Soc. 126 (9): 2820–8. doi:10.1021/ja037233l. PMID 14995199. 
59. ^ Masgrau L., Roujeinikova A., Johannissen L. O., Hothi P., Basran J., Ranaghan K. E., Mulholland A. J., Sutcliffe M. J., Scrutton N. S., Leys D. (2006). "Atomic Description of an Enzyme Reaction Dominated by Proton Tunneling". Science 312 (5771): 237–41. doi:10.1126/science.1126002. PMID 16614214. 
60. ^ Cleland, W.W. (1963). "The Kinetics of Enzyme-catalyzed Reactions with two or more Substrates or Products 2. {I}nhibition: Nomenclature and Theory". Biochim. Biophys. Acta 67: 173–87. 
61. ^ Price, NC. (1979). "What is meant by ‘competitive inhibition’?". Trends in Biochemical Sciences 4: pN272. 
62. ^ Poulin R, Lu L, Ackermann B, Bey P, Pegg AE. Mechanism of the irreversible inactivation of mouse ornithine decarboxylase by alpha-difluoromethylornithine. Characterization of sequences at the inhibitor and coenzyme binding sites. J Biol Chem. 1992 January 5;267(1):150–8. PMID 1730582
63. ^ Yoshikawa S and Caughey WS. (15 May 1990). "Infrared evidence of cyanide binding to iron and copper sites in bovine heart cytochrome c oxidase. Implications regarding oxygen reduction". J Biol Chem. 265 (14): 7945–58. PMID 2159465. http://www.jbc.org/cgi/reprint/265/14/7945. 
64. ^ Hunter T. (1995). "Protein kinases and phosphatases: the yin and yang of protein phosphorylation and signaling". Cell. 80 (2): 225–36. doi:10.1016/0092-8674(95)90405-0. PMID 7834742. 
65. ^ Berg JS, Powell BC, Cheney RE (1 April 2001). "A millennial myosin census". Mol. Biol. Cell 12 (4): 780–94. PMID 11294886. PMC 32266. http://www.molbiolcell.org/cgi/content/full/12/4/780. 
66. ^ Meighen EA (1 March 1991). "Molecular biology of bacterial bioluminescence". Microbiol. Rev. 55 (1): 123–42. PMID 2030669. PMC 372803. http://mmbr.asm.org/cgi/reprint/55/1/123?view=long&pmid=2030669. 
67. ^ Mackie RI, White BA (1 October 1990). "Recent advances in rumen microbial ecology and metabolism: potential impact on nutrient output". J. Dairy Sci. 73 (10): 2971–95. PMID 2178174. http://jds.fass.org/cgi/reprint/73/10/2971. 
68. ^ Faergeman NJ, Knudsen J (April 1997). "Role of long-chain fatty acyl-CoA esters in the regulation of metabolism and in cell signalling". Biochem. J. 323 (Pt 1): 1–12. PMID 9173866. PMC 1218279. http://www.biochemj.org/bj/323/0001/bj3230001.htm. 
69. ^ Doble B. W., Woodgett J. R. (April 2003). "GSK-3: tricks of the trade for a multi-tasking kinase". J. Cell. Sci. 116 (Pt 7): 1175–86. doi:10.1242/jcs.00384. PMID 12615961. http://jcs.biologists.org/cgi/content/full/116/7/1175. 
70. ^ Carr C. M., Kim P. S. (April 2003). "A spring-loaded mechanism for the conformational change of influenza hemagglutinin". Cell 73 (4): 823–32. doi:10.1016/0092-8674(93)90260-W. PMID 8500173. 
71. ^ Phenylketonuria: NCBI Genes and Disease. Retrieved 4 April 2007.
72. ^ Renugopalakrishnan V, Garduno-Juarez R, Narasimhan G, Verma CS, Wei X, Li P. (2005). "Rational design of thermally stable proteins: relevance to bionanotechnology". J Nanosci Nanotechnol. 5 (11): 1759–1767. doi:10.1166/jnn.2005.441. PMID 16433409. 
73. ^ Hult K, Berglund P. (2003). "Engineered enzymes for improved organic synthesis". Curr Opin Biotechnol. 14 (4): 395–400. doi:10.1016/S0958-1669(03)00095-8. PMID 12943848. 
74. ^ Jiang L, Althoff EA, Clemente FR (March 2008). "De novo computational design of retro-aldol enzymes". Science (journal) 319 (5868): 1387–91. doi:10.1126/science.1152692. PMID 18323453. 
75. ^ Guzmán-Maldonado H, Paredes-López O (September 1995). "Amylolytic enzymes and products derived from starch: a review". Critical reviews in food science and nutrition 35 (5): 373–403. doi:10.1080/10408399509527706. PMID 8573280. 
76. ^ Dulieu C, Moll M, Boudrant J, Poncelet D (2000). "Improved performances and control of beer fermentation using encapsulated alpha-acetolactate decarboxylase and modeling". Biotechnology progress 16 (6): 958–65. doi:10.1021/bp000128k. PMID 11101321. 

Further reading

Etymology and history "New Beer in an Old Bottle: Eduard Buchner and the Growth of Biochemical Knowledge, edited by Athel Cornish-Bowden and published by Universitat de València (1997): ISBN 84-370-3328-4". Archived from the original on 2008-02-07. http://web.archive.org/web/20080207101706/http://bip.cnrs-mrs.fr/bip10/buchner.htm. , A history of early enzymology. Williams, Henry Smith, 1863–1943. A History of Science: in Five Volumes. Volume IV: Modern Development of the Chemical and Biological Sciences, A textbook from the 19th century. Kleyn J, Hough J (1971). "The microbiology of brewing". Annu. Rev. Microbiol. 25: 583–608. doi:10.1146/annurev.mi.25.100171.003055. PMID 4949040.  Enzyme structure and mechanism Fersht, Alan (1999). Structure and mechanism in protein science: a guide to enzyme catalysis and protein folding. San Francisco: W.H. Freeman. ISBN 0-7167-3268-8.  Walsh C (1979). Enzymatic reaction mechanisms. San Francisco: W. H. Freeman. ISBN 0-7167-0070-0.  Page, M. I., and Williams, A. (Eds.). Enzyme Mechanisms. Royal Society of Chemistry, 1987. ISBN 0-85186-947-5. Bugg, T. Introduction to Enzyme and Coenzyme Chemistry. (2nd edition), Blackwell Publishing Limited, 2004. ISBN 1-40511-452-5. Warshel, A. Computer Modeling of Chemical Reactions in enzymes and Solutions. John Wiley & Sons Inc., 1991. ISBN 0-471-18440-3. Thermodynamics "Reactions and Enzymes" Chapter 10 of on-line biology book at Estrella Mountain Community College.

Kinetics and inhibition Cornish-Bowden, Athel. Fundamentals of Enzyme Kinetics. (3rd edition), Portland Press, 2004. ISBN 1-85578-158-1. Segel Irwin H. Enzyme Kinetics: Behavior and Analysis of Rapid Equilibrium and Steady-State Enzyme Systems. (New Ed edition), Wiley-Interscience, 1993. ISBN 0-471-30309-7. Baynes, John W. Medical Biochemistry. (2nd edition), Elsevier-Mosby, 2005. ISBN 0-7234-3341-0, p. 57. Function and control of enzymes in the cell Price, N. and Stevens, L. Fundamentals of Enzymology: Cell and Molecular Biology of Catalytic Proteins. Oxford University Press, 1999. ISBN 0-19-850229-X. "Nutritional and Metabolic Diseases". Chapter of the on-line textbook Introduction to Genes and Disease from the NCBI. Enzyme-naming conventions Enzyme Nomenclature, Recommendations for enzyme names from the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology. Koshland, D. The Enzymes, v. I, ch. 7. Acad. Press, New York, 1959. Industrial applications "History of industrial enzymes", Article about the history of industrial enzymes from the late 1900s to the present times.

External links

Wikimedia Commons has media related to: Enzymes

• Structure/Function of Enzymes, Web tutorial on enzyme structure and function.
• Enzymes in diagnosis Role of enzymes in diagnosis of diseases.
• Enzyme spotlight Monthly feature at the European Bioinformatics Institute on a selected enzyme.
• AMFEP, Association of Manufacturers and Formulators of Enzyme Products
• BRENDA database, a comprehensive compilation of information and literature references about all known enzymes; requires payment by commercial users.
• Enzyme Structures Database links to the known 3-D structure data of enzymes in the Protein Data Bank.
• ExPASy enzyme database, links to Swiss-Prot sequence data, entries in other databases and to related literature searches.
• KEGG: Kyoto Encyclopedia of Genes and Genomes Graphical and hypertext-based information on biochemical pathways and enzymes.
• MACiE database of enzyme reaction mechanisms.
• MetaCyc database of enzymes and metabolic pathways
• Face-to-Face Interview with Sir John Cornforth who was awarded a Nobel Prize for work on stereochemistry of enzyme-catalyzed reactions Freeview video by the Vega Science Trust
• Sigma Aldrich Enzyme Assays by Enzyme Name – Hundreds of assays sorted by enzyme name.
• Bugg TD (October 2001). "The development of mechanistic enzymology in the 20th century". Nat Prod Rep 18 (5): 465–93. doi:10.1039/b009205n. PMID 11699881. http://rsc.org/delivery/_ArticleLinking/DisplayArticleForFree.cfm?doi=b009205n&JournalCode=NP. 

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v • d • e Proteins: enzymes Topics Active site - Allosteric regulation - Binding site - Catalytically perfect enzyme - Coenzyme - Cofactor - Cooperativity - EC number Enzyme catalysis - Enzyme inhibitor - Enzyme kinetics - Lineweaver–Burk plot - Michaelis–Menten kinetics - List of enzymes Types EC1 Oxidoreductases/list - EC2 Transferases/list - EC3 Hydrolases/list - EC4 Lyases/list - EC5 Isomerases/list - EC6 Ligases/list

This entry is from Wikipedia, the leading user-contributed encyclopedia. It may not have been reviewed by professional editors (see full disclaimer)

Dansk (Danish)
n. - enzym

Nederlands (Dutch)
enzym (versneller van biochemische processen)

Français (French)
n. - enzyme

Deutsch (German)
n. - Enzym

Ελληνική (Greek)
n. - (βιολ.) ένζυμο

Italiano (Italian)
enzima

Português (Portuguese)
n. - enzima (f) (Med.)

Русский (Russian)
энзим

Español (Spanish)
n. - enzima

Svenska (Swedish)
n. - enzym

中文（简体）(Chinese (Simplified))
酵素

中文（繁體）(Chinese (Traditional))
n. - 酵素

한국어 (Korean)
n. - 효소

日本語 (Japanese)
n. - 酵素

العربيه (Arabic)
‏(الاسم) خميرة, إنزين‏

עברית (Hebrew)
n. - ‮חלבון הפועל כזרז בריאקציה כימית מסוימת, חומר מתסיס, אנזים‬

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